Merge pull request #3 from aTrotier/noClipExample

No clip example

README.md

@@ -37,3 +37,10 @@ cmap = relaxationColorMap("T1")
 VIEW(x,c=cmap) # Do not use range limits here! 
 ```
 <p>Again, "VIEW" refers to your favorite viewing software.</p>
+<p><br>If the simplified processing is invoked WITH use of range limits, then the 
+distinction is lost between invalid values and low-but-valid values. See second image in the 
+example below: it represents a circular object with a T1 value that is gradually increasing
+from top to bottom, but only valid within a circular "object", the outside thereof representing 
+unknown T1 values. </p>
+
+![image info](./rangeNoRange.jpg)

docs/src/example.md

@@ -10,32 +10,45 @@ The generated colormap can be easily integrated with multiple plotting library l
 For `Makie.jl` the colormap can be directly used like `heatmap(x,colormap=cmap,colorrange=(loLev,upLev))`
 
 ```@example 2
-using FileIO
-using Downloads
 using qMRIColors
 using CairoMakie
 
-url = "https://github.com/mfuderer/colorResources/raw/refs/heads/main/sampleT1map.jld"
-dest_path = "sampleT1map.jld"
-# Download the file
-Downloads.download(url, dest_path)
-x = FileIO.load("sampleT1map.jld")["sampleT1map"]
+# -----  Make test object: gradually increasing T1, but invalid outside a circle
+size = 256; center = size÷2+1; radius = 100; origin = CartesianIndex(center,center)
+d(x::CartesianIndex, y::CartesianIndex) = √( (x[1]-y[1])^2 + (x[2]-y[2])^2 )
+row = [10*i for i in 1:size]
+testT1= zeros(size,size)
+testT1 .= row
 
+# Set invalid values to 0
+allidx = CartesianIndices(testT1)
+invalid = allidx[ d.(origin, allidx) .> radius];
+testT1[invalid] .= 0
+# ---------------------------------------------- Test object made
+
+# -------------------- Display test object the correct and the wrong way
 loLev = 700
-upLev = 1500
-cmap,imClip = relaxationColorMap("T1",x,loLev,upLev)
+upLev = 2000
 begin
   f=CairoMakie.Figure()
-  ax=Axis(f[1,1],aspect = DataAspect(),title = "clip")
+  ax=Axis(f[1,1],aspect = DataAspect(),title = "Using imClip")
+  cmap,imClip = relaxationColorMap("T1",testT1,loLev,upLev)
   h=heatmap!(ax,rotr90(imClip),colormap=cmap,colorrange=(loLev,upLev))
   Colorbar(f[1,2],h)
   hidedecorations!(ax)
 
-  ax=Axis(f[2,1],aspect = DataAspect(),title = "no clip")
-  h=heatmap!(ax,rotr90(x),colormap=cmap,colorrange=(loLev,upLev))
+  ax=Axis(f[2,1],aspect = DataAspect(),title = "wrong: simplified, \n with range")
+  cmap = relaxationColorMap("T1")
+  h=heatmap!(ax,rotr90(testT1),colormap=cmap,colorrange=(loLev,upLev))
   Colorbar(f[2,2],h)
   hidedecorations!(ax)
 
+  ax=Axis(f[3,1],aspect = DataAspect(),title = "OK: simplified, \n no range")
+  cmap = relaxationColorMap("T1")
+  h=heatmap!(ax,rotr90(testT1),colormap=cmap)
+  Colorbar(f[3,2],h)
+  hidedecorations!(ax)
+
   # clean up plot
   colsize!(f.layout, 1, Aspect(1,1))
   resize_to_layout!(f)
@@ -49,8 +62,14 @@ end
 Using GR backend
 ```@example 3
 using FileIO
+using Downloads
 using qMRIColors
+using CairoMakie
 
+url = "https://github.com/mfuderer/colorResources/raw/refs/heads/main/sampleT1map.jld"
+dest_path = "sampleT1map.jld"
+# Download the file
+Downloads.download(url, dest_path)
 x = FileIO.load("sampleT1map.jld")["sampleT1map"]
 
 loLev = 700